I'm not convinced that it's a ground loop because the intercom system
has a single-point ground. I have the system grounded where at least
SOME other avionics are grounded, but not sure that all avionics are
grounded at that point

Lift that single ground ground and verify with a continuity test that
with power off, the intercom system is now floating. Make sure there
there isn't some other sneak path to ground that you don't know about.

The frequency of the alternator whine isn't so high that it would be
capacitively coupling into all but high impedance circuits.

If it is noise is present on the B+ line, it should be present at both
headset locations, and a simple power supply filter should take care of
it.

I'd be suspicious of the ground/common connection between the
alternator and the battery. It should be done only with heavy wires,
and not involve the airframe to carry the alternator current.

Another ground loop vs B+ capacitive coupling check - does the whine
become worse as the alternator load is increased, say by turning on
pitot heat and the landing lights? If so, it is more likely a ground
problem.